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dbSNPNormalized (snp-normalizer)
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de.hu.berlin.wbi.objects</FONT>
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Class dbSNPNormalized</H2>
<PRE>
<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>
  <IMG SRC="../../../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">de.hu.berlin.wbi.objects.dbSNP</A>
      <IMG SRC="../../../../../resources/inherit.gif" ALT="extended by "><B>de.hu.berlin.wbi.objects.dbSNPNormalized</B>
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<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A>&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>&gt;</DD>
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<DL>
<DT><PRE>public class <B>dbSNPNormalized</B><DT>extends <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A><DT>implements <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A>&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>&gt;</DL>
</PRE>

<P>
Represents a <CODE>Mutation</CODE> mention which has been successfully
 normalized to a <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects"><CODE>dbSNP</CODE></A> . Therefore it extends <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects"><CODE>dbSNP</CODE></A>.
<P>

<P>
<DL>
<DT><B>Author:</B></DT>
  <DD>Philippe Thomas</DD>
</DL>
<HR>

<P>

<!-- ======== CONSTRUCTOR SUMMARY ======== -->

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<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html#dbSNPNormalized(de.hu.berlin.wbi.objects.dbSNP, boolean, boolean, boolean, de.hu.berlin.wbi.objects.UniprotFeature, boolean)">dbSNPNormalized</A></B>(<A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>&nbsp;dbsnp,
                boolean&nbsp;exactMatch,
                boolean&nbsp;methioneMatch,
                boolean&nbsp;psm,
                <A HREF="../../../../../de/hu/berlin/wbi/objects/UniprotFeature.html" title="class in de.hu.berlin.wbi.objects">UniprotFeature</A>&nbsp;feature,
                boolean&nbsp;alleleOrder)</CODE>

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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
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<CODE>&nbsp;int</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html#compareTo(de.hu.berlin.wbi.objects.dbSNPNormalized)">compareTo</A></B>(<A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>&nbsp;that)</CODE>

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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
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<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;int</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html#getConfidence()">getConfidence</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
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<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;boolean</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html#isAlleleOrder()">isAlleleOrder</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns true if Alleles are in the same order in dbSNP as in the text mention</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;boolean</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html#isExactMatch()">isExactMatch</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;boolean</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html#isFeatureMatch()">isFeatureMatch</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;boolean</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html#isMethioneMatch()">isMethioneMatch</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;boolean</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html#isPsm()">isPsm</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html#toString()">toString</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(non-Javadoc)</TD>
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</TABLE>
&nbsp;<A NAME="methods_inherited_from_class_de.hu.berlin.wbi.objects.dbSNP"><!-- --></A>
<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
<TH ALIGN="left"><B>Methods inherited from class de.hu.berlin.wbi.objects.<A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A></B></TH>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD><CODE><A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html#equals(java.lang.Object)">equals</A>, <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html#getAaPosition()">getAaPosition</A>, <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html#getGeneID()">getGeneID</A>, <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html#getHgvs()">getHgvs</A>, <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html#getResidues()">getResidues</A>, <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html#getRsID()">getRsID</A>, <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html#getSNP(int)">getSNP</A>, <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html#getWildtype()">getWildtype</A>, <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html#hashCode()">hashCode</A>, <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html#init(de.hu.berlin.wbi.objects.DatabaseConnection, java.lang.String, java.lang.String)">init</A>, <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html#setAaPosition(int)">setAaPosition</A>, <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html#setGeneID(int)">setGeneID</A>, <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html#setHgvs(java.util.Set)">setHgvs</A>, <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html#setResidues(java.util.Set)">setResidues</A>, <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html#setRsID(int)">setRsID</A></CODE></TD>
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<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>
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<TD><CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>
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<P>

<!-- ========= CONSTRUCTOR DETAIL ======== -->

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<A NAME="dbSNPNormalized(de.hu.berlin.wbi.objects.dbSNP, boolean, boolean, boolean, de.hu.berlin.wbi.objects.UniprotFeature, boolean)"><!-- --></A><H3>
dbSNPNormalized</H3>
<PRE>
public <B>dbSNPNormalized</B>(<A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>&nbsp;dbsnp,
                       boolean&nbsp;exactMatch,
                       boolean&nbsp;methioneMatch,
                       boolean&nbsp;psm,
                       <A HREF="../../../../../de/hu/berlin/wbi/objects/UniprotFeature.html" title="class in de.hu.berlin.wbi.objects">UniprotFeature</A>&nbsp;feature,
                       boolean&nbsp;alleleOrder)</PRE>
<DL>
<DL>
<DT><B>Parameters:</B><DD><CODE>dbsnp</CODE> - <DD><CODE>exactMatch</CODE> - <DD><CODE>methioneMatch</CODE> - <DD><CODE>psm</CODE> - <DD><CODE>feature</CODE> - <DD><CODE>alleleOrder</CODE> - </DL>
</DL>

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<B>Method Detail</B></FONT></TH>
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<A NAME="toString()"><!-- --></A><H3>
toString</H3>
<PRE>
public <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>
<DL>
<DD>(non-Javadoc)
<P>
<DD><DL>
<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html#toString()">toString</A></CODE> in class <CODE><A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A></CODE></DL>
</DD>
<DD><DL>
<DT><B>See Also:</B><DD><A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html#toString()"><CODE>dbSNP.toString()</CODE></A></DL>
</DD>
</DL>
<HR>

<A NAME="isAlleleOrder()"><!-- --></A><H3>
isAlleleOrder</H3>
<PRE>
public boolean <B>isAlleleOrder</B>()</PRE>
<DL>
<DD>Returns true if Alleles are in the same order in dbSNP as in the text mention
<P>
<DD><DL>
</DL>
</DD>
<DD><DL>
</DL>
</DD>
</DL>
<HR>

<A NAME="isExactMatch()"><!-- --></A><H3>
isExactMatch</H3>
<PRE>
public boolean <B>isExactMatch</B>()</PRE>
<DL>
<DD><DL>
</DL>
</DD>
<DD><DL>

<DT><B>Returns:</B><DD>true if the normalization required no heuristics</DL>
</DD>
</DL>
<HR>

<A NAME="isMethioneMatch()"><!-- --></A><H3>
isMethioneMatch</H3>
<PRE>
public boolean <B>isMethioneMatch</B>()</PRE>
<DL>
<DD><DL>
</DL>
</DD>
<DD><DL>

<DT><B>Returns:</B><DD>true if position has an offset of +/-1</DL>
</DD>
</DL>
<HR>

<A NAME="isFeatureMatch()"><!-- --></A><H3>
isFeatureMatch</H3>
<PRE>
public boolean <B>isFeatureMatch</B>()</PRE>
<DL>
<DD><DL>
</DL>
</DD>
<DD><DL>
</DL>
</DD>
</DL>
<HR>

<A NAME="isPsm()"><!-- --></A><H3>
isPsm</H3>
<PRE>
public boolean <B>isPsm</B>()</PRE>
<DL>
<DD><DL>
</DL>
</DD>
<DD><DL>

<DT><B>Returns:</B><DD>true if snp is a protein sequence mutation</DL>
</DD>
</DL>
<HR>

<A NAME="getConfidence()"><!-- --></A><H3>
getConfidence</H3>
<PRE>
public int <B>getConfidence</B>()</PRE>
<DL>
<DD><DL>
</DL>
</DD>
<DD><DL>

<DT><B>Returns:</B><DD>confidence for Normalization</DL>
</DD>
</DL>
<HR>

<A NAME="compareTo(de.hu.berlin.wbi.objects.dbSNPNormalized)"><!-- --></A><H3>
compareTo</H3>
<PRE>
public int <B>compareTo</B>(<A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>&nbsp;that)</PRE>
<DL>
<DD><DL>
<DT><B>Specified by:</B><DD><CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Comparable.html?is-external=true#compareTo(T)" title="class or interface in java.lang">compareTo</A></CODE> in interface <CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A>&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>&gt;</CODE></DL>
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